Perhaps the clearest illustration of the role of theories is the basic scientific enterprise of categorization. We have a long history of organizing the world we observe into categories. Our choices of categories reflect implicit and explicit assumptions about what things “matter,” what similarities are relevant. These assumptions are the results of theories. We have grouped all living things into kingdoms and then into phyla or divisions. We group animals by species. The groupings are based upon a variety of assumptions about what things are similar. For example, we identify animals with backbones as a meaningful group (“vertebrates”). We could have decided that relevant groupings were by color (everything that is red), by weight or by height. Indeed for other purposes, color, weight and height are relevant criteria for grouping things. All of these activities are based upon models or theories about the world.
Deductive theories
It is commonly accepted that the most powerful and versatile of theories are deductive in structure.7 They contain a set of assumptions or premises (or axioms) followed by a set of rules for derivation or logical manipulation (sometimes called rules of transformation), so that one can draw conclusions of the form if A, then B, but often in far more complex structures with many variables. Such deductive theories can allow a variety of more remote identification (or prediction) of the consequences of specified starting conditions. However, nothing “new” is introduced—the subsequent implications are all contained in the initial axioms or assumptions, given the rules governing the manipulation of the axioms and the derivation of additional propositions. Deductive theories of this type generally lend themselves to formalization, specifically often to mathematical representation. Indeed, such theories can be viewed, and could have started life, as purely logical constructs. In fact, a good deductive theory will necessarily be a good logical construct. The question that arises is whether or how a deductive system bears any relationship with the external, real world.
Of interest here are theories that tie to or incorporate real, observable data or events—theories about the world in which we live. Such theories must contain what are called “contingent propositions”—statements about the world that are subject to verification or observation or, in other words, statements that can be “true” or “false”. See Richard Bevan Braithwaite, Scientific Explanation (Cambridge University Press, 1968), p.24. Thus, a theory would include contingent propositions, and an observer could attempt to ascertain whether those contingent propositions are true in the circumstances at hand. If so, then one could presumably make predictions (deductive inferences) that also included contingent propositions. Such inferences would be logically necessary within the theory (or deductive system). Such predictions could also be “tested” against real world data or used (relied upon) in real world applications.
In all events, it is crucial to be able to recognize when terms used in a theory merely appear to reference actual things (or are carelessly assumed to reference actual things) and when the theories contain real contingent propositions. A formal deductive system can be expressed in symbols. The symbols could be given names that are used in normal conversation to refer to physical objects.8 However, to tie the deductive system to the physical world, one needs also to introduce into the system logical propositions utilizing the “things” to which the names refer and that contain some factual (non-circular and not purely definitional) relationships that are subject to empirical testing—in other words, assertions that have some real content concerning the physical world.
There are terms that have meaning only in the context of the theory or the logical structure. An illustration set out by philosopher Gilbert Ryle is from the vocabulary of games. The word “trump” has no meaning out of the context of bridge, and one cannot explain its meaning without some explanation of the rules of that game. Dilemmas (1954), p.33. Another matter that deserves attention, to avoid misunderstandings, is the use in theories of terms that have an ordinary usage but technical meanings in the context of the theory, such as the “mass” or the “temperature” of an object. The technical meanings are defined by the theory. As Ryle explained, “technical terms … are theory-laden, laden, that is, not just with theoretical luggage of some sort or other but with the luggage of…theory. Their meanings change with changes in the theory. Knowing their meanings requires some grasp of the theory.” Id., p.90.
At some level, all words are “theory-laden,” that is based upon or reflecting models of the physical world that people use to comprehend their environment. Obviously, it is important at least to identify and communicate the particular models involved in statements made, in order to avoid misunderstandings and miscommunications.
Modern scientific theories regularly make use of terms or concepts that are not subject to direct sensory observation. A frequently cited example is the “electron.” It is an assumed or hypothesized “object” defined by several characteristics, including a negative electrical charge. The catalogue of characteristics defines the term functionally and enables it to be utilized in theories of atomic and molecular structures. Obviously, the related theories have been very successful and powerful. But, does an electron actually “exist”? See, e.g., Brian Greene, The Elegant Universe (2005), pp.108–16. This example will be discussed further in a later chapter.
An example: The gene
Perhaps a more vivid and suggestive example is the concept of the “gene.” In the 1860s, the Moravian monk Gregor Mendel, in his famous experiments with hybrid peas, crossing round with wrinkly and yellow with green peas, discovered patterns of heredity. Subsequently, the experimental data were expressed in a theory of “genes” expressing recessive and dominant traits, with which we are all at least passingly familiar.9 The second half of the twentieth century brought the emergence of molecular biology, with the “discovery” of DNA in 1953, and then RNA and so on.
One might have expected that these breakthroughs would lead to a physical identification of the “gene” within the cell structure, that is, that we would be able to identify objects (by chemical composition and structural location) that constitute the gene that is the transmitter of hereditable traits. Instead, biologists seem to have discovered that the gene, as previously conceived, does not exist. Instead, heritable traits are transmitted by a variety of types of quite complex processes and elements contained within the cell. See, e.g., The Stanford Encyclopedia of Philosophy, “Gene” (revised 2009).
Interestingly, however, the Mendelian genetic theory is still a good—indeed, perhaps the most effective—method of predicting the inheritance of traits. In addition, we have been able to ascertain that the human genome consists of only about 20,000 genes, not much more than many other life forms of complexity greater than the bacteria (and far fewer than had been expected when the human genome project began). We can also identify numerous genes that a variety of quite different animals have in common. See Frank Ryan, Virolution (2009), p.2. Thus, the theory is eminently useful. It appears that the concept of a gene reflects various bundles of processes and cell constituents that as a bundle function just as the supposed gene. In addition, different traits are transmitted by considerably different bundles—some much more complicated than others.
So, is the theory based upon genes true or false?
One answer is to say that the Mendelian theory reflects a higher level or macro view of the phenomena while molecular biology is dealing with a more granular or micro level of activity. The assumption would be that when the theories have been perfected, they would both be capable of generating the same predictions or inferences at the level of the organism, but that the micro level theories would be able to explain many details that the macro theory would not even perceive as existing. It would then be the